I said I would so here you are, a shedload of misc suggestions. I hope some are useful and workable but I'm sure the final product will be great regardless and I'm super hyped 
(It might seem strange to post this before 1) a suggestions forum and 2) actually seeing any gameplay but I've always said that the early bird gets the worm)
Types of War/Alliance
In other games wars and alliances haven't had many dimensions. Sure there have been limited wars in HOI, and defensive alliances (though these are decided by the AI) in EU4, but it might be cool to have a dropdown on both the war and alliance options in diplomacy;
Wars
Cold War - Units will not automatically fight when they otherwise would, though small battles can occur if either side chooses. If a 'tension' meter increases too high then the war type will jump up. Benefits for some ethos might include decreased dissent (rallying the people against a common foe) and diplomacy bonuses with other rivals of the enemy. It should only be possible between peer opponents.
Intervention - Can only occur during a war with one of your allies/protectorates/etc. Your side can only fight enemy units in allied territory or military installations. Think Coalition activities in iraq and syria right now.
Limited War - In this kind of war taking systems would be very expensive but battles would provide a lot of warscore. Diplomacy maluses would be smaller and this would be acceptable to peace-loving races or federations which could otherwise kick up a big fuss. Things like planetary bombardment or NBC weapons during a limited war cause MASSIVE ae. Allies might be more willing to join a limited war.
Total War - standard fare in paradox games. Take a bunch of systems, change their governments, enforce various demands. This should not be easy for peaceful species to call for. Nasty weapons are employed.
War of Annihilation - No quarter. No warscore; the only end is when one side is wiped out. Warlike species/machine species would find this a lot easier to get than others.
Alliances
Non-aggression pact - already mentioned in previews.
Alliance of convenience - Only a small relations bonus but allows all the trade/movement benefits of an alliance but the factions will not feel too pressed to join in a real war. Only possible when very threatened. Not much ae/relations malus when broken.
Defensive alliance - Only calls the allies to war if DOWed, not if you DOW.
Alliance - As per usual.
One-sided alliance - A more powerful faction can call for this. Smaller factions will usually only agree when really threatened. They will send all their units to join the big faction's military but if any enemy units sneak past or damage the small faction's economy they will be really unhappy. Good for hegemonies.
Orbital bombardments
Maybe this requires a special ship weapon? Anyway, the idea is that when you have ships capable of this around a planet, you go to a dropdown and choose several options; single strike, supporting bombardment, bombardment, "BDZ". Some events could result in terrorist cells or dangerous phenomena on planets which are best resolved by a single strike. Supporting bombardment would occur while landing an invasion force and increase their chance of success. A bombardment would involve massively decreasing the population and productivity of a 'tile' which would almost certainly cow the planet into submission.
'BDZ' would require a lot of ships but result in a dead planet. Nothing but rocks and dust. Just imagine the AE and dissent it would bring to your country...
Planet shields could be a counter. Maybe two types; one which acts kinda like a fort in other paradox games, having a chance to break at each tick, and one which is unbreakable- but allows nothing in or out, so eventually the attackers will watch the shield fall away from lack of power and see the people below long starved. Unless they are machines...
'Fallen Empire' alternatives
Having all the one-planet advanced civs represented by the fallen empire model feels a bit limited. What about;
1) Worlds where they never bothered with/got space travel and so just happened to keep advancing on one planet.
2) Worlds covered by VR cubicles as the people have long ago created their own reality.
3) Worlds which don't want to be bothered by all the mucky civs around the universe and have invented some kind of 'cloaking device' for the planet which only very advanced players could detect.
Migrant Factions
If not all factions were planetbound, that would be cool (particularly for modders). Maybe there is a feature which means they spawn around a mothership or 'craftworld' and generally rely on asteroids etc to create new stuff, including new motherships.
Populations
Overpopulation could be a big problem particularly on plain old planets. If the governor doesn't keep things under control then crime, dissent, factionalism, resource stretching, and general trouble will come into play. Perhaps the governor can choose between population 'policies' or be forced to create new colonies/start a few wars/soylent green.
Alien suggestions
Why not.
1) Various plant derived forms. Inspiration from Venus Fly Traps, walking palms, buoyant kelp...
2) Aquatic aliens. A lot of scripting would be needed to deal with the differences I guess.
3) Living starships. Probably bioengineered, of course. Rogue, or friendly, or acting like mercenaries (Spline anyone?)
Megastructures
Completely necessary. Really hard to build. The amount of mass required should be a limiting factor, you literally have to deconstruct planets to build them. I'm pretty sure I saw mass units as a quantity for each planet so this would tie in well. You unlock each with a tech card but it takes a long time 1) to gather the mass requirement from planets/asteroids using either special ships or some handwavy nanodissemblers and 2) to put it together, but it yields enormous resources and can support a tonne of population.
Maybe the 'province model' of Stellaris prohibits this but I hope it is possible.
Suggestions by increasing mass;
1) Orbitals in honour of the late Iain M. Banks. A thousands-of-km diameter ring which is positioned in orbit around a star and goes around on its merry way.
2) Rings. Like Ringworld, encircles a star. Requires handwavy materials but whatever.
3) Dyson cloud. Surrounds the star with solar stations, enormous amounts of energy.
Big Dumb Weapons
All complete fantasy.
1) Engineered cross-species plagues that cause problems for centuries to come and any scientists or explorers visiting the planet can get screwed over. An event chain can lead them to finding the creators... welp.
2) Orbit changing thrusters. Attach a tonne of these and send a planet either hurtling into the sun, out into the cold, or even use it as a giant spaceship (remember the Dalek Invasion of the Earth?) of course if the people on it get unhappy it will be easy for them to stop the process.
3) Planet crackers. Some handwavy core resonance nonsense that shatters the planet. Debris very good for making megastructures.
4) Supernova weapons. Boom.
(It might seem strange to post this before 1) a suggestions forum and 2) actually seeing any gameplay but I've always said that the early bird gets the worm)Types of War/Alliance
In other games wars and alliances haven't had many dimensions. Sure there have been limited wars in HOI, and defensive alliances (though these are decided by the AI) in EU4, but it might be cool to have a dropdown on both the war and alliance options in diplomacy;
Wars
Cold War - Units will not automatically fight when they otherwise would, though small battles can occur if either side chooses. If a 'tension' meter increases too high then the war type will jump up. Benefits for some ethos might include decreased dissent (rallying the people against a common foe) and diplomacy bonuses with other rivals of the enemy. It should only be possible between peer opponents.
Intervention - Can only occur during a war with one of your allies/protectorates/etc. Your side can only fight enemy units in allied territory or military installations. Think Coalition activities in iraq and syria right now.
Limited War - In this kind of war taking systems would be very expensive but battles would provide a lot of warscore. Diplomacy maluses would be smaller and this would be acceptable to peace-loving races or federations which could otherwise kick up a big fuss. Things like planetary bombardment or NBC weapons during a limited war cause MASSIVE ae. Allies might be more willing to join a limited war.
Total War - standard fare in paradox games. Take a bunch of systems, change their governments, enforce various demands. This should not be easy for peaceful species to call for. Nasty weapons are employed.
War of Annihilation - No quarter. No warscore; the only end is when one side is wiped out. Warlike species/machine species would find this a lot easier to get than others.
Alliances
Non-aggression pact - already mentioned in previews.
Alliance of convenience - Only a small relations bonus but allows all the trade/movement benefits of an alliance but the factions will not feel too pressed to join in a real war. Only possible when very threatened. Not much ae/relations malus when broken.
Defensive alliance - Only calls the allies to war if DOWed, not if you DOW.
Alliance - As per usual.
One-sided alliance - A more powerful faction can call for this. Smaller factions will usually only agree when really threatened. They will send all their units to join the big faction's military but if any enemy units sneak past or damage the small faction's economy they will be really unhappy. Good for hegemonies.
Orbital bombardments
Maybe this requires a special ship weapon? Anyway, the idea is that when you have ships capable of this around a planet, you go to a dropdown and choose several options; single strike, supporting bombardment, bombardment, "BDZ". Some events could result in terrorist cells or dangerous phenomena on planets which are best resolved by a single strike. Supporting bombardment would occur while landing an invasion force and increase their chance of success. A bombardment would involve massively decreasing the population and productivity of a 'tile' which would almost certainly cow the planet into submission.
'BDZ' would require a lot of ships but result in a dead planet. Nothing but rocks and dust. Just imagine the AE and dissent it would bring to your country...
Planet shields could be a counter. Maybe two types; one which acts kinda like a fort in other paradox games, having a chance to break at each tick, and one which is unbreakable- but allows nothing in or out, so eventually the attackers will watch the shield fall away from lack of power and see the people below long starved. Unless they are machines...
'Fallen Empire' alternatives
Having all the one-planet advanced civs represented by the fallen empire model feels a bit limited. What about;
1) Worlds where they never bothered with/got space travel and so just happened to keep advancing on one planet.
2) Worlds covered by VR cubicles as the people have long ago created their own reality.
3) Worlds which don't want to be bothered by all the mucky civs around the universe and have invented some kind of 'cloaking device' for the planet which only very advanced players could detect.
Migrant Factions
If not all factions were planetbound, that would be cool (particularly for modders). Maybe there is a feature which means they spawn around a mothership or 'craftworld' and generally rely on asteroids etc to create new stuff, including new motherships.
Populations
Overpopulation could be a big problem particularly on plain old planets. If the governor doesn't keep things under control then crime, dissent, factionalism, resource stretching, and general trouble will come into play. Perhaps the governor can choose between population 'policies' or be forced to create new colonies/start a few wars/soylent green.
Alien suggestions
Why not.
1) Various plant derived forms. Inspiration from Venus Fly Traps, walking palms, buoyant kelp...
2) Aquatic aliens. A lot of scripting would be needed to deal with the differences I guess.
3) Living starships. Probably bioengineered, of course. Rogue, or friendly, or acting like mercenaries (Spline anyone?)
Megastructures
Completely necessary. Really hard to build. The amount of mass required should be a limiting factor, you literally have to deconstruct planets to build them. I'm pretty sure I saw mass units as a quantity for each planet so this would tie in well. You unlock each with a tech card but it takes a long time 1) to gather the mass requirement from planets/asteroids using either special ships or some handwavy nanodissemblers and 2) to put it together, but it yields enormous resources and can support a tonne of population.
Maybe the 'province model' of Stellaris prohibits this but I hope it is possible.
Suggestions by increasing mass;
1) Orbitals in honour of the late Iain M. Banks. A thousands-of-km diameter ring which is positioned in orbit around a star and goes around on its merry way.
2) Rings. Like Ringworld, encircles a star. Requires handwavy materials but whatever.
3) Dyson cloud. Surrounds the star with solar stations, enormous amounts of energy.
Big Dumb Weapons
All complete fantasy.
1) Engineered cross-species plagues that cause problems for centuries to come and any scientists or explorers visiting the planet can get screwed over. An event chain can lead them to finding the creators... welp.
2) Orbit changing thrusters. Attach a tonne of these and send a planet either hurtling into the sun, out into the cold, or even use it as a giant spaceship (remember the Dalek Invasion of the Earth?) of course if the people on it get unhappy it will be easy for them to stop the process.
3) Planet crackers. Some handwavy core resonance nonsense that shatters the planet. Debris very good for making megastructures.
4) Supernova weapons. Boom.
